There is no direct connection from Lima to Pucusana. However, you can take the subway to Villa El Salvador then take the taxi to Pucusana. Alternatively, you can take the subway to Villa El Salvador then take the taxi to Pucusana.
Visited Pucusana via Viator booking from Lima. It was a 5 hour tour in a comfortable minivan. Stopped on the way at a local bakery where bread is cooked in clay ovens. Very popular with the locals and very clean bathrooms. The village was a working fishing port with colorful boats every where.